The San Mateo Creek Basin in New Mexico, USA is located within the Grants Mineral Belt-an area with numerous uranium (U) ore deposits, mines, and milling operations. Six monitoring wells set in an alluvial aquifer near the Homestake Mining Co. Superfund site in the lower San Mateo Creek Basin were logged with a suite of borehole geophysical tools including spectral gamma-ray (SGR), vertically profiled with passive samplers for U and selenium (Se) concentrations, and purged sampled for same constituents. The integrated approach allowed for an assessment on the role of heterogeneity (both physical and chemical) in determining U concentrations in groundwater. Uranium, as measured with SGR logging, is ubiquitous in the alluvial aquifer and the underlying Chinle Group. Aqueous U concentrations appear to be inversely related to thorium (Th) concentrations, as measured by the SGR log, indicating the possibility that U is bound in or adsorbed to clays in the aquifer. The stratigraphy of the alluvium likely plays a role in elevated concentrations of aqueous U. Interbedded clay and sand layers allow for the mobilization of U in oxic sandy layers from U adsorbed in sediments in reduced clay layers. The stratigraphy also plays a role in the degree of mixing of groundwater in the formation and well. Mixing can obscure the ability to identify U sources. Mixing is exacerbated by the relatively long screens (> 20 ft long or > 6.1 m) of the monitoring wells.